Contacts of the helix formed by residues 362 - 372 (chain C) in PDB entry 4U1D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 362 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297C LEU* 4.1 3.7 - - - +
338C ASP* 3.3 16.8 - - - +
360C LYS 5.2 1.3 - - - +
361C PRO* 1.3 78.2 - - - +
363C ARG* 1.3 60.1 + - - +
364C LYS* 3.1 11.0 + - - +
365C GLU* 2.7 48.0 + - + +
366C MET* 2.9 27.4 + - - +
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Residues in contact with ARG 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C LEU* 4.1 10.0 - - - +
332C ALA 3.7 9.6 + - - +
333C ILE* 2.8 38.8 + - - +
335C THR* 3.2 43.7 + - + -
336C GLN 3.6 9.9 - - - +
337C LEU* 3.5 19.5 - - - +
338C ASP* 3.1 19.8 + - - +
339C GLU* 4.5 3.7 + - + +
362C THR* 1.3 74.6 - - - +
364C LYS* 1.3 62.8 + - + +
366C MET* 3.7 1.5 - - - +
367C LEU* 2.9 37.2 + - - +
392C GLU* 2.7 40.8 + - - +
427C VAL* 4.2 3.8 - - - +
431C ARG* 2.8 19.4 - - - +
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Residues in contact with LYS 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.6 25.0 + - - +
338C ASP* 4.7 0.6 + - - +
362C THR* 3.1 8.4 + - - +
363C ARG* 1.3 86.3 - - + +
365C GLU* 1.3 59.9 + - + +
367C LEU* 3.3 8.5 + - - +
368C GLN* 2.9 56.3 + - + +
392C GLU* 5.8 4.7 - - - +
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Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 5.5 6.2 - - - -
360C LYS 4.8 0.7 - - - +
361C PRO* 3.6 14.8 - - + +
362C THR* 2.7 49.6 + - + +
364C LYS* 1.3 76.1 - - + +
366C MET* 1.3 57.4 + - - +
368C GLN* 3.2 10.2 + - - +
369C SER* 2.9 30.6 + - - -
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Residues in contact with MET 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C LEU* 3.5 27.6 - - + +
300C THR* 3.6 32.8 - - + +
301C THR* 3.3 24.2 - - - +
304C LYS* 3.5 29.4 - - - +
332C ALA* 4.3 6.7 - - + -
357C LEU* 5.7 0.4 - - + -
361C PRO* 4.1 23.8 - - + +
362C THR 2.9 16.3 + - - +
363C ARG* 3.7 4.0 - - - +
365C GLU* 1.3 75.3 - - - +
367C LEU* 1.3 58.3 + - - +
369C SER* 2.7 20.1 + - - -
370C ILE* 3.0 24.1 + - + +
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C PHE* 3.6 25.8 - - + -
332C ALA* 3.6 35.4 - - + +
333C ILE* 3.9 9.0 - - + +
363C ARG* 2.9 33.3 + - - +
364C LYS* 3.7 6.5 - - - +
366C MET* 1.3 76.5 - - - +
368C GLN* 1.3 58.7 + - + +
370C ILE* 3.3 4.2 + - - +
371C ILE* 3.0 33.7 + - + +
388C TYR* 3.5 30.7 - - + +
392C GLU* 4.0 23.1 - - + +
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Residues in contact with GLN 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C LYS* 2.9 48.8 + - + +
365C GLU* 3.7 8.2 - - - +
367C LEU* 1.3 74.1 - - + +
369C SER* 1.3 55.9 + - - +
370C ILE 3.0 5.4 - - - -
371C ILE* 3.7 11.7 - - + +
372C GLU* 2.9 37.6 + - + +
388C TYR* 5.4 4.5 + - - +
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Residues in contact with SER 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LYS* 2.7 35.1 + - - -
365C GLU 2.9 13.6 + - - -
366C MET* 2.7 19.3 + - - -
368C GLN* 1.3 74.9 - - - +
370C ILE* 1.3 56.7 + - - +
372C GLU* 4.4 11.6 - - - +
373C ASP* 3.5 22.1 + - - +
376C ILE* 5.2 0.5 - - - +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C THR* 3.7 10.8 - - + -
304C LYS* 4.0 16.2 - - + -
328C ILE* 3.6 26.2 - - + +
329C PHE* 3.8 24.0 - - + -
332C ALA* 3.6 31.0 - - + -
366C MET* 3.0 13.6 + - + +
367C LEU 3.5 6.7 - - - +
368C GLN 3.0 0.6 - - - -
369C SER* 1.3 80.3 - - - +
371C ILE* 1.3 64.2 + - - +
372C GLU 3.3 0.4 + - - -
373C ASP* 3.5 12.3 - - - +
376C ILE* 4.0 24.8 - - + +
377C TYR* 3.5 16.7 + - + +
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C PHE* 3.8 17.3 - - + -
367C LEU 3.0 25.0 + - - +
368C GLN* 3.1 10.0 + - + +
370C ILE* 1.3 76.9 - - - +
372C GLU* 1.3 61.6 + - - +
374C GLU* 3.6 8.5 - - - +
377C TYR* 3.4 42.3 - - + +
388C TYR* 3.3 48.5 - - + +
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Residues in contact with GLU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C GLN* 2.9 17.6 + - + +
369C SER* 4.7 7.8 - - - -
371C ILE* 1.3 76.6 - - - +
373C ASP* 1.3 61.3 + - - +
374C GLU* 3.0 19.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il